We present high-resolution simulations of high velocity clouds (HVCs) colliding with the outer part of the Galactic disk. All of the simulations include a 3 × 108 M ⊙ dark matter subhalo. Three simulations model a dark matter subhalo without a gaseous component, while eight simulations model a dark matter subhalo accompanied by a gaseous cloud of mass 2–8 × 106 M ⊙. Half of the simulations include the coherent component of the Galaxy's magnetic field. Each simulation spans ∼40 million years before the collision and ∼40 million years after the collision. The collisions between the gas cloud and disk splash gas into the halo, punch half-kiloparsec-size holes in the disk, and form long-lived, multi-kiloparsec-size shells. Each shell encloses a bubble of relatively cool gas. Holes and shells of these scales would be observable, and some have been observed in the past. We determine the fate of the HVC gas, temperature, composition, and ionization state of the bubble and shell gas, size and longevity of the holes, and effects of cloud density. Simulations show that the clouds do not survive the chaos of passage through the disk, but instead become part of the splash, bubble, and shell. Some dark matter clouds may appear to carry material with them long after the collision, but this material is shell gas that was captured by the dark matter subhalo. These results have ramifications for the Smith Cloud and other clouds hypothesized to have hit the Galactic disk.